1) Designated Constructions++, failing that, the ablity to choose to add constructions to the end or beginning of the job queue, instead of always most-recent first.
2) Division of 'Masonry' into 'Stone Cutting' and 'Brick Laying', because I want my lengendary masons to make nice furnature instead of crawling out onto rickity catwalks to build things with no quality modifiers.
3) Prioritized job assignments: Dwarfs active jobs in a reorderable list instead of just on/off toggle, So that Urist will only do his secondary job is there is nothing to do for the first, then the third... and so on.
4) Triggered production scripts is one I've been thinking about for a while: If stock of ___ goes [below/above] ## add job to make ## of ___. This would require office workers be active, only an active bookkeeper could detect the stock changes to initiate the request, and then sends it to a manager to schedule it. Each rule would need a (file) cabinet to track it, and a bookkeeper would take some amount of (skill dependant) time to process each check, looping through the list of rules. Maybe insert a quick stop at the local noble for a quick approval check, and for Bureaucratic Fun, and if paper/documents are introduced have interoffice mail hauling jobs to actually shuffle the requests around.
5) Pipes built like axels/gearings to move water. would require pressure to work effectivly, which I think would exclude Magma, which should be harder to work with anyway.
6) I like the Schools idea, but I think what would be more suitable is an apprenticeship program. The ability to assign dwarven children to an adult to watch them work; gaining some skill in whatever their assigned teacher does. This would allow some control of what moodable skills they might get before maturity. Don't know if having the student should slow down (due to having to explain things), or speed up (due to an extra pair of hands) the jobs being done, so I would save leave it at a balance, unmodified.
7) The ability (if it dosn't already exist) to have multiple simultainous forts in the same world; so if nothing else you could 'multithread' by running several forts at once. (Possibly requiring that forts can't get to far ahead of each other, like syncing up at season changes.)
8) Have Small Animal Dissection/Animal Care enable the neutering of pets.
9) As a prerequisite/option for the above, have the ability to have jobs require certain skill levels; that is, not set at playtime like a workshop profiles, but something set in the raws so that the job won't even appear as an option until you have a dwarf with sufficent skill for example, only a Master 'Small Animal Dissector' or above can even try to do a neutering.
10) Allow Medical skills to be Moodable! "Doctor Victor Frankenurist looses a roaring laughter, fell and terrible!" (OK, I ran out of ideas.)
edit:
0) Have haulers haul more than one item at a time; maybe requiring carrying a bin/backpack with them and putting related items in it. "I'm hauling a sock (or other item) from Point A to Stockpile B; I am not overencumbered; and there is another sock (or other item that is accepted by the destination stockpile) less than 2 (or distance between Point A and Stockpile B / 10) steps away from point A, so I'll grab that as well."